caa a22 4500 606190414 CHVBK 20210128100855.0 cr unu---uuuuu 210128e20150901xx s 000 0 eng 10.1007/s10577-015-9484-6 doi (NATIONALLICENCE)springer-10.1007/s10577-015-9484-6 Short interspersed DNA elements and miRNAs: a novel hidden gene regulation layer in zebrafish? [Elektronische Daten] [Margherita Scarpato, Claudia Angelini, Ennio Cocca, Maria Pallotta, Maria Morescalchi, Teresa Capriglione] In this study, we investigated by in silico analysis the possible correlation between microRNAs (miRNAs) and Anamnia V-SINEs (a superfamily of short interspersed nuclear elements), which belong to those retroposon families that have been preserved in vertebrate genomes for millions of years and are actively transcribed because they are embedded in the 3′ untranslated region (UTR) of several genes. We report the results of the analysis of the genomic distribution of these mobile elements in zebrafish (Danio rerio) and discuss their involvement in generating miRNA gene loci. The computational study showed that the genes predicted to bear V-SINEs can be targeted by miRNAs with a very high hybridization E-value. Gene ontology analysis indicates that these genes are mainly involved in metabolic, membrane, and cytoplasmic signaling pathways. Nearly all the miRNAs that were predicted to target the V-SINEs of these genes, i.e., miR-338, miR-9, miR-181, miR-724, miR-735, and miR-204, have been validated in similar regulatory roles in mammals. The large number of genes bearing a V-SINE involved in metabolic and cellular processes suggests that V-SINEs may play a role in modulating cell responses to different stimuli and in preserving the metabolic balance during cell proliferation and differentiation. Although they need experimental validation, these preliminary results suggest that in the genome of D. rerio, as in other TE families in vertebrates, the preservation of V-SINE retroposons may also have been favored by their putative role in gene network modulation. Springer Science+Business Media Dordrecht, 2015 Retrotransposons nationallicence SINEs nationallicence miRNA nationallicence 3′UTR nationallicence ChIP-Seq : Chromatin immunoprecipitation coupled with high-throughput sequencing nationallicence FDR : False discovery rate nationallicence GO : Gene ontology nationallicence LINE : Long interspersed element nationallicence LTR : Long terminal repeat nationallicence MIR : Mammalian interspersed repeat nationallicence miRNA : microRNA nationallicence SINE : Short interspersed nuclear element nationallicence SRP : Signal recognition particle nationallicence TE : Transposable element nationallicence UTR : Untraslated region nationallicence Scarpato Margherita IGB "Adriano Buzzati-Traverso” CNR, via P. Castellino, 80131, Napoli, Italy aut Angelini Claudia Istituto per le Applicazioni del Calcolo "M. Picone”, CNR, via P. Castellino, 80131, Napoli, Italy aut Cocca Ennio IBBR-CNR, via P. Castellino, 80131, Napoli, Italy aut Pallotta Maria Dipartimento di Biologia, Università di Napoli Federico II, via Cinthia 21, 80126, Napoli, Italy aut Morescalchi Maria Dipartimento di Biologia, Università di Napoli Federico II, via Cinthia 21, 80126, Napoli, Italy aut Capriglione Teresa Dipartimento di Biologia, Università di Napoli Federico II, via Cinthia 21, 80126, Napoli, Italy aut Chromosome Research Springer Netherlands 23/3(2015-09-01), 533-544 0967-3849 23:3<533 2015 23 10577 https://doi.org/10.1007/s10577-015-9484-6 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s10577-015-9484-6 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Scarpato Margherita IGB "Adriano Buzzati-Traverso” CNR, via P. Castellino, 80131, Napoli, Italy aut NATIONALLICENCE 700 1- Angelini Claudia Istituto per le Applicazioni del Calcolo "M. Picone”, CNR, via P. Castellino, 80131, Napoli, Italy aut NATIONALLICENCE 700 1- Cocca Ennio IBBR-CNR, via P. Castellino, 80131, Napoli, Italy aut NATIONALLICENCE 700 1- Pallotta Maria Dipartimento di Biologia, Università di Napoli Federico II, via Cinthia 21, 80126, Napoli, Italy aut NATIONALLICENCE 700 1- Morescalchi Maria Dipartimento di Biologia, Università di Napoli Federico II, via Cinthia 21, 80126, Napoli, Italy aut NATIONALLICENCE 700 1- Capriglione Teresa Dipartimento di Biologia, Università di Napoli Federico II, via Cinthia 21, 80126, Napoli, Italy aut NATIONALLICENCE 773 0- Chromosome Research Springer Netherlands 23/3(2015-09-01), 533-544 0967-3849 23:3<533 2015 23 10577